Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for RPLP0
Basic gene info.Gene symbolRPLP0
Gene nameribosomal protein, large, P0
SynonymsL10E|LP0|P0|PRLP0|RPP0
CytomapUCSC genome browser: 12q24.2
Genomic locationchr12 :120634502-120639014
Type of geneprotein-coding
RefGenesNM_001002.3,
NM_053275.3,
Ensembl idENSG00000089157
Description60S acidic ribosomal protein P060S ribosomal protein L10Eacidic ribosomal phosphoprotein P0
Modification date20141207
dbXrefs MIM : 180510
HGNC : HGNC
Ensembl : ENSG00000089157
HPRD : 01610
Vega : OTTHUMG00000169317
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPLP0
BioGPS: 6175
Gene Expression Atlas: ENSG00000089157
The Human Protein Atlas: ENSG00000089157
PathwayNCI Pathway Interaction Database: RPLP0
KEGG: RPLP0
REACTOME: RPLP0
ConsensusPathDB
Pathway Commons: RPLP0
MetabolismMetaCyc: RPLP0
HUMANCyc: RPLP0
RegulationEnsembl's Regulation: ENSG00000089157
miRBase: chr12 :120,634,502-120,639,014
TargetScan: NM_001002
cisRED: ENSG00000089157
ContextiHOP: RPLP0
cancer metabolism search in PubMed: RPLP0
UCL Cancer Institute: RPLP0
Assigned class in ccmGDBC

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Phenotypic Information for RPLP0(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPLP0
Familial Cancer Database: RPLP0
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: RPLP0
MedGen: RPLP0 (Human Medical Genetics with Condition)
ClinVar: RPLP0
PhenotypeMGI: RPLP0 (International Mouse Phenotyping Consortium)
PhenomicDB: RPLP0

Mutations for RPLP0
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPLP0 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG180012PPP3CB30587107523084475239128RPLP058167112120634509120634606
AF155662RPLP04121012120634611120635169NDUFA13209721191962704219639007
AI765188RPLP02720612120634505120634684MTMR10201470153125108831253198
BE698288RPLP017512120636993120637174CDS1659048552277785522802
AF132973RPLP04121612120634611120635175NDUFA13217718191962705219639006
BC000673RTEL1101349206228971362305447RPLP01344172212120634505120635270

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr12:120634697-120634697p.A278G2
chr12:120636469-120636469p.I180S2
chr12:120635197-120635197p.S240S2
chr12:120636777-120636777p.A115A1
chr12:120637273-120637273p.Y24N1
chr12:120634627-120634627p.K301K1
chr12:120635248-120635248p.A223A1
chr12:120636935-120636935p.L102L1
chr12:120638562-120638562p.W9R1
chr12:120634635-120634635p.E299K1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 31 5 1  421 114 5
# mutation13 31 5 1  431 114 5
nonsynonymous SNV11 21 2 1  33   13 5
synonymous SNV 2 1  3    1 1 1 1  
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr12:120635152p.T255T,RPLP02
chr12:120635197p.S240S,RPLP02
chr12:120637168p.F138L,RPLP01
chr12:120635143p.T258T,RPLP01
chr12:120636435p.F137L,RPLP01
chr12:120637201p.V121A,RPLP01
chr12:120636466p.E254Q,RPLP01
chr12:120637225p.L102L,RPLP01
chr12:120635157p.A250V,RPLP01
chr12:120636469p.I98S,RPLP01

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for RPLP0 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for RPLP0

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

EEF1G,RPL10,RPL10A,RPL11,RPL13A,RPL18A,RPL27A,
RPL36,RPL37A,RPL4,RPL6,RPL7A,RPLP0,RPLP1,
RPLP2,RPS10,RPS18,RPS2,RPS8,RPSA,RPSAP58
EEF1B2,EEF1G,EIF3D,GNB2L1,IMPDH2,NOB1,RPL10,
RPL10A,RPL12,RPL14,RPL37,RPL4,RPL6,RPLP0,
RPS18,RPS2,RPS5,RPS6,RPS7,RPS8,RPSAP58

LRRC75A-AS1,RPL10A,RPL12,RPL13A,RPL18,RPL35,RPL36,
RPL41,RPL7A,RPLP0,RPLP1,RPS11,RPS14,RPS15,
RPS16,RPS19,RPS29,RPS3,RPS5,RPS8,RPS9
AHCY,PHB2,RPL10,RPL13A,RPL18,RPL18A,RPL19,
RPL29,RPL32,RPL7A,RPL8,RPLP0,RPLP1,RPS11,
RPS14,RPS3,RPS5,RPS6,RPS8,RPSA,RPSAP58
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for RPLP0


There's no related Drug.
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Cross referenced IDs for RPLP0
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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